Re: [Ifeffit] Fwd: Feff calc

Hi Josh, Thanks a lot for your answer and help! Yes, indeed these last 3 atoms should not be there; they were created automatically by symmetry when I ran atoms and forgot to take them out Now it does work nicely! Thanks again. Cheers, Gemma -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of joshua jason kas Sent: Wednesday, June 11, 2008 10:10 PM To: John J. Rehr Cc: ifeffit@millenia.cars.aps.anl.gov; Gemma Guilera Subject: Re: [Ifeffit] Fwd: Feff calc Hi Gemma, This error basically comes from the fact that you have two very different types of oxygen atoms in your system, but only one potential. In this case the oxygen potential and muffin tin radius is being defined by the oxygen that is bonded directly to the Rh atom. This gives a relatively large muffin tin radius which, when used at the other oxygen sites, overlaps too much with the carbon muffin tins. The way to fix this is to give the two types of oxygens different potentials, i.e. POTENTIALS * ipot Z element 0 45 Rh 1 17 Cl 2 6 C 3 8 O 4 8 O ATOMS 0.000000 0.000000 0.000000 0 Rh1 0.000000 1 0.066250 -1.715140 -0.175300 2 C1_1 1.725348 2 1.699390 0.099230 -0.398490 2 C2_1 1.748304 3 -0.109490 2.041000 0.145210 3 O3_1 2.049086 4 -2.233040 -0.277590 0.571930 1 Cl1_1 2.321773 5 0.063490 -2.904610 -0.348340 4 O1_1 2.926112 6 2.880780 0.195790 -0.586340 4 O2_1 2.946357 7 -3.609490 2.682000 -4.216430 3 O3_2 6.164400 8 -6.320060 0.195790 1.175470 3 O2_2 6.431425 9 -1.485940 5.000590 -4.643160 1 Cl1_2 6.983756 10 END The above input file runs, but I would be a bit concerned about the last three atoms in the list, since they so far away from everything else. Are they really supposed to be there? Cheers, Josh Kas On Sat, 7 Jun 2008, John J. Rehr wrote:

Hi Josh,

Are you familiar with this error msg? If not, could you check it out? It comes up fairly often.

Thanks. J.

---------- Forwarded message ---------- Date: Thu, 5 Jun 2008 09:33:40 -0400 From: Bruce Ravel To: XAFS Analysis Using Ifeffit , Gemma Guilera Subject: [Ifeffit] Fwd: Feff calc

Hi Gemma,

I don't know what that error message from Feff means either, so I am forwarding this along to the Ifeffit mailing list in hopes that someone else -- maybe someone from John's group -- can explain.

If I had to guess, I would say that there was a problem constructing the muffin tins either because the atom list is so short or because the atoms are too far apart. The muffin tin algorithm does presume that the atoms will not be separated by unphysically large distances, as the last three atoms in your list are.

It would seem that you are using some version of Feff8 -- is that correct? It woul have been helpful had you identified the version of Feff you are using and had you captured the screen output from Feff to a file. It usually helps you receive the answer you are looking for if you provide as much context as possible.

B

---------- Forwarded Message ----------

Subject: Feff calc Date: Thursday 05 June 2008 From: "Gemma Guilera" To: bravel@anl.gov

Dear Bruce,

I was trying to run a FEFF calculation (herein attached) and I got a message telling me to ask you to INCREASE NOVP.

To be honest, I don't know what is this and why it could not run (maybe there is something wrong on the feff.inp file or maybe it is correct that I need to increase such 'NOVP'), but here I am.

I would be really grateful if you could give me a hand so I can continue with my calculations.

Thanks a lot and have a nice day,

Gemma

* This feff6 input file was generated by Atoms 3.0.1 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001

* -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu*x=1: 500.60 microns, unit edge step: 622.91 microns * specific gravity = 0.620 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction: 0.00020 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *

* ----------------------------------------------------------------- * The following crystallographic data were used: * * title [Rh(CO)2ClO] * space = P 21/c * a = 9.3680 b = 13.410 c = 18.2710 * alpha = 90.0 beta = 100.840 gamma = 90.0 * core = Rh1 edge = K * atoms * ! elem x y z tag occ * Cl -0.04060 0.19680 0.13880 Cl1 1.00000 * C 0.20930 0.30400 0.12200 C1 1.00000 * C 0.38680 0.16870 0.12690 C2 1.00000 * O 0.20900 0.39270 0.11250 O1 1.00000 * O 0.51520 0.16150 0.12900 O2 1.00000 * O 0.19020 0.02390 0.13770 O3 1.00000 * Rh 0.20210 0.17610 0.13090 Rh1 1.00000 * -----------------------------------------------------------------

TITLE [Rh(CO)2ClO]

* Rh K edge (23220.0 eV), second number is S0^2 EDGE K S02 1.0

* pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3

*** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0

* r_scf [ l_scf n_scf ca ] SCF 4.0 1

RMAX 7.0 EXAFS

POTENTIALS * ipot Z element 0 45 Rh 1 17 Cl 2 6 C 3 8 O

ATOMS * this list contains 10 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Rh1 0.00000 0.06625 -1.71514 -0.17530 2 C1_1 1.72535 1.69939 0.09923 -0.39849 2 C2_1 1.74830 -0.10949 2.04100 0.14521 3 O3_1 2.04909 -2.23304 -0.27759 0.57193 1 Cl1_1 2.32177 0.06349 -2.90461 -0.34834 3 O1_1 2.92611 2.88078 0.19579 -0.58634 3 O2_1 2.94636 -3.60949 2.68200 -4.21643 3 O3_2 6.16440 -6.32006 0.19579 1.17547 3 O2_2 6.43142 -1.48594 5.00059 -4.64316 1 Cl1_2 6.98376 END

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-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973

My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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